7EO4: Sphingosine 1-phosphate receptor 1

Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to BAF312. Determined by electron microscopy at 2.86 Å resolution. Released 5 Jan 2022.

Method: Electron microscopy
Resolution: 2.86 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,302
Mol. weight: 155.93 kDa
Ligands: J8C
Released: 5 Jan 2022

Explore 7EO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EO4 contains 28 α-helices and 59 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	23-32	10
α-helix	47-71	25
α-helix	74-76	3
α-helix	79-104	26
α-helix	106-108	3
α-helix	114-145	32
α-helix	159-175	17
α-helix	188-190	3
α-helix	200-232	33
α-helix	255-280	26
α-helix	290-292	3
α-helix	297-313	17
α-helix	316-322	7

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-38	6	1
α-helix	47-50	4
β-strand	185-191	7	1
β-strand	194-200	7	1
β-strand	220-222	3	1
α-helix	251-254	4
β-strand	265	1	1
α-helix	331-350	20

Chain C: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	30-33	4
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-169	5	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	241-245	5	7
β-strand	250-254	5	7
α-helix	255-257	3
β-strand	259-264	6	7
β-strand	273-275	3	8
β-strand	285-287	3	9
β-strand	288-289	2	8
β-strand	294	1	10
β-strand	295-297	3	9
β-strand	308	1	10
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	49-51	3
α-helix	56-58	3

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	15-25	11	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-86	9	11
β-strand	92-99	8	12
β-strand	110-111	2	12
β-strand	115-119	5	12
β-strand	128-130	3	13
β-strand	134-136	3	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
α-helix	184	1
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	213-219	7	14
α-helix	225	1
β-strand	227	1	14
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sphingosine 1-phosphate receptor 1	A	protein	382	Homo sapiens	P21453 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	247	Homo sapiens

Sequence of entity 1 (A), FASTA

>7EO4_1 Sphingosine 1-phosphate receptor 1 (chains A)
MGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISADKENSIKLTSVVFILICCFII
LENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTYKLTPAQWFLR
EGSMFVALSASVWSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVISLILGGLPIM
GWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYCRIYSLVRTRSRRLTFRKN
ISKASRSSEKSLALLKTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDILFRAEYFLVLA
VLNSGTNPIIYTLTNKEMRRAFIRIMSCCKCPSGDSAGKFKRPIIAGMEFSRSKSDNSSH
PQKDEGDNPETIMSSGNVNSSS

Sequence of entity 2 (B), FASTA

>7EO4_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>7EO4_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>7EO4_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>7EO4_5 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
J8C	1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methy…	C29 H35 F3 N2 O3	1

Primary citation

Structural basis of sphingosine-1-phosphate receptor 1 activation and biased agonism. Xu, Z., Ikuta, T., Kawakami, K. et al. Nat Chem Biol (2022) 18:281-288. DOI 10.1038/s41589-021-00930-3 · PubMed

Other PDB entries of the same protein (UniProt P21453 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TD4 2.6 Å, Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod
9VNZ 2.79 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with HY-X-1011
9VO0 2.79 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with Ponesimod
3V2Y 2.8 Å, Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A
7VIF 2.83 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with (S)-FTY720-P
7VIE 2.86 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with S1P
7EO2 2.89 Å, Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to FTY720p
7VIG 2.89 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307
9VO1 2.97 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with SAR247799
7EVY 2.98 Å, Cryo-EM structure of siponimod -bound Sphingosine-1-phosphate receptor 1 in complex with…
7VIH 2.98 Å, Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CBP-307
7TD3 3.0 Å, Sphingosine-1-phosphate receptor 1-Gi complex bound to S1P

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